TMA36 RNA Seq dataset: Indolent vs. Intermediate vs. Aggressive
Mafe Senosain
2021-01-27
Pre-processing of the data
Exploring data
Batch effect correction
Clust on Eigen GENES
## Warning: Missing column names filled in: 'X1' [1]##
## ── Column specification ────────────────────────────────────────────────────────
## cols(
## .default = col_double(),
## X1 = col_character()
## )
## ℹ Use `spec()` for the full column specifications.
Deconvolution data
XCell
## Warning in wilcox.test.default(c(0, 0, 0, 0.0148, 0, 0.0106, 0, 0, 0, 0.0046:
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0.0148, 0, 0.0106, 0, 0, 0, 0.0046:
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.0062, 0, 0, 0, 0.0033, 0, 0.0027, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0014, 0, 0, 0.1452, 0, 0, 0, 0, 0.0413:
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0014, 0, 0, 0.1452, 0, 0, 0, 0, 0.0413:
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0.1, 0.0208, 0, 0, 0, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.047, 0.3325, 0, 0.008, 0, 0.7011, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.047, 0.3325, 0, 0.008, 0, 0.7011, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.1244, 0, 0.1337, 0.0027, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0214, 0.0684, 0, 0, 0.0094, 0.0816, 0.1816, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0214, 0.0684, 0, 0, 0.0094, 0.0816, 0.1816, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0432, 0.0046, 0.0073, 0, 0.0072, 0.1808, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0162, 0.0216, 0, 0, 0, 0.1458, 0.0464, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0162, 0.0216, 0, 0, 0, 0.1458, 0.0464, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0.0124, 0.003, 0, 0.0048, 0.0452, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0462, 0.0199, 0.0679, 0, 0.0132, 0, 0.0849, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0462, 0.0199, 0.0679, 0, 0.0132, 0, 0.0849, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0539, 0.0317, 0.0367, 0.0138, 0, 0.0144, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0444, 0.1224, 0.0231, 0, 0.0289, 0, 0.1765, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0444, 0.1224, 0.0231, 0, 0.0289, 0, 0.1765, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0823, 0.0105, 0.0285, 0.0397, 0.0174, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0645, 0.0708, 0, 0.0107, 0, 0.3989, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0645, 0.0708, 0, 0.0107, 0, 0.3989, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.0179, 0.0116, 0.0438, 0.0134, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0979, 0.0715, 0.0074, 0.0529, 0.003, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0979, 0.0715, 0.0074, 0.0529, 0.003, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.004, 0, 0.0707, 0, 0.0468, 0.0922, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.1136, 0.0612, 0, 0.0182, 0, 0.2938, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.1136, 0.0612, 0, 0.0182, 0, 0.2938, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0299, 0, 0.0293, 0.0042, 0.0326, 0.0499, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.1205, 0.059, 0, 0, 0, 0.3162, 0.0364, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.1205, 0.059, 0, 0, 0, 0.3162, 0.0364, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0147, 0, 0.0436, 0, 0.0452, 0.0128, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0536, 0, 0, 0, 0, 0.0568, 0, 0, 0), :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0536, 0, 0, 0, 0, 0.0568, 0, 0, 0), :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0148, 0, 0, 0, 0, 0.0084, 0, 0.0057, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0241, 0.0185, 0, 0.0016, 0, 0.1114, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0241, 0.0185, 0, 0.0016, 0, 0.1114, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(3e-04, 0, 0, 0.0307, 0, 0.0024, 0, 0, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0082, 0.0382, 0.0118, 0.0023, 0.002, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0082, 0.0382, 0.0118, 0.0023, 0.002, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0036, 0.0082, 0.0067, 0.0424, 0.0107, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0.0099, 0.0093, 0.0112, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0.0099, 0.0093, 0.0112, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.0078, 0, 0.002, 0.0088, 7e-04, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0465, 0.0375, 0.1193, 0.062, 0.1813, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0465, 0.0375, 0.1193, 0.062, 0.1813, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.1219, 0, 0, 0.0835, 0.0913, 0.1353, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0305, 0.0627, 0.17, 0, 0.0113, 0, 0.264, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0305, 0.0627, 0.17, 0, 0.0113, 0, 0.264, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0346, 0.0136, 0.1095, 0, 0.0743, 0.031, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0325, 0.0112, 0.0092, 0, 0.0215, 0, 0.0493, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0325, 0.0112, 0.0092, 0, 0.0215, 0, 0.0493, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.004, 5e-04, 0.0078, 0.002, 0.0472, 0.0053, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0674, 0.0211, 0.0657, 0.312, 0.1087, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0674, 0.0211, 0.0657, 0.312, 0.1087, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0551, 0.0865, 0.0992, 0, 0.0906, 0.1233, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0072, 7e-04, 0.004, 0, 6e-04, 0.0066, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0072, 7e-04, 0.004, 0, 6e-04, 0.0066, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(1e-04, 0, 4e-04, 0, 0, 0, 0, 0, 0, 0, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.2682, 0.1802, 0.1939, 0.0429, 0.0468, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.2682, 0.1802, 0.1939, 0.0429, 0.0468, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.2541, 0.2147, 0.1835, 0.2557, 0.1848, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), c(0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), c(0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.1243, 0.1254, 0.2513, 0.2366, 0.3984, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.1243, 0.1254, 0.2513, 0.2366, 0.3984, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0653, 0.0146, 0.1667, 0, 0, 0.2687, 0.1263, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.0174, 0.0374, 0.0143, 0, 0.0049, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.0174, 0.0374, 0.0143, 0, 0.0049, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.0213, 0, 0.0349, 0.0044, 0, 0.0209, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.1181, 0.0492, 0.0967, 0.4638, 0.0369, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.1181, 0.0492, 0.0967, 0.4638, 0.0369, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.1312, 0.1179, 0.4502, 0.088, 0.2164, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0014, 0, 0, 0, 2e-04, 0.0049, 0, 0, 0.0036, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0014, 0, 0, 0, 2e-04, 0.0049, 0, 0, 0.0036, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0042, 0.0023, 0, 0, 0, 0.0052, 0.0025, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0204, 0.014, 0.0079, 2e-04, 0, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0204, 0.014, 0.0079, 2e-04, 0, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.019, 0.0096, 0.0081, 0.0164, 0.012, 0.013, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0175, 0.033, 0.002, 0.009, 0.0034, 0.0128, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0175, 0.033, 0.002, 0.009, 0.0034, 0.0128, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0506, 0.0319, 0.0205, 0.0919, 0.0107, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), c(0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), c(0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0581, 0.1851, 0, 0, 0.2228, 0, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0581, 0.1851, 0, 0, 0.2228, 0, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0114, 0.1019, 0.0088, 0, 0, 0.2994, 0.0329, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0584, 0.1664, 0.045, 0.0952, 0.1077, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0584, 0.1664, 0.045, 0.0952, 0.1077, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0244, 0.0083, 0.0313, 0, 0.0774, 0.0074, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0359, 0.1077, 0.0195, 0.0077, 0.035, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0359, 0.1077, 0.0195, 0.0077, 0.035, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.017, 0.0021, 0.022, 3e-04, 0.0291, 0.0035, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0371, 0.0204, 0.0132, 0.1458, 0.0674, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0371, 0.0204, 0.0132, 0.1458, 0.0674, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0208, 0.0116, 0.0143, 0.0029, 0.0632, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0138, 0.0442, 0.0721, 0.074, 0.0514, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0138, 0.0442, 0.0721, 0.074, 0.0514, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0127, 0.0215, 0.0504, 0.0436, 0.0663, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0024, 0, 0.0012, 0.0228, 0, 0.0217, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0024, 0, 0.0012, 0.0228, 0, 0.0217, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0023, 0.0032, 0, 0.0037, 9e-04, 0.0047, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0037, 0.0045, 0.0019, 0, 0.0069, 0, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0037, 0.0045, 0.0019, 0, 0.0069, 0, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0081, 0.0069, 0.003, 0, 0, 9e-04, 0.0029, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.0907, 0, 0, 0, 0.2741, 0, 0, 0), :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.0907, 0, 0, 0, 0.2741, 0, 0, 0), :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.002, 0, 0.0396, 0, 0, 0, 0.0391, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0.0227), c(0.0127, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0.0227), c(0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.0472, 0, 0, 0, 0, 0, 0, 0, 0, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 6e-04, 0, 0.0493, 0.0594, 0, 0.1855, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 6e-04, 0, 0.0493, 0.0594, 0, 0.1855, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0.0161, 0.0044, 0, 0, 0.0069, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0081, 0.0022, 0.0165, 0.0212, 0, 0.0303, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0081, 0.0022, 0.0165, 0.0212, 0, 0.0303, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0144, 0.0239, 0.005, 0.0231, 0.014, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0035, 0, 0, 0, 0, 0.0252, 0, 0, 0), :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0035, 0, 0, 0, 0, 0.0252, 0, 0, 0), :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0714, 0.0445, 0.0401, 0.019, 0.0675, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0714, 0.0445, 0.0401, 0.019, 0.0675, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0456, 0.0249, 0.0137, 0, 0.02, 0.0669, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.003, 0, 0.0016, 0.0025, 0.0019, 0.0027, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.003, 0, 0.0016, 0.0025, 0.0019, 0.0027, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(7e-04, 0.0014, 7e-04, 7e-04, 0.0013, 0.001, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0016, 0, 0, 0.0132, 0, 0.0118, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0016, 0, 0, 0.0132, 0, 0.0118, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 1e-04, 0, 0.0032, 0, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0756, 0.0403, 0.0137, 0, 0, 0, 0.0188, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0756, 0.0403, 0.0137, 0, 0, 0, 0.0188, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.1068, 0.0979, 0.02, 0.1521, 0, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.1386, 0.0708, 0.1995, 0, 0.3062, 0.0192, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.1386, 0.0708, 0.1995, 0, 0.3062, 0.0192, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0117, 0.0595, 0, 0, 0.2039, 0.0868, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0114, 0.0428, 0.0373, 0, 4e-04, 0, 0.1265, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0114, 0.0428, 0.0373, 0, 4e-04, 0, 0.1265, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0353, 0.034, 0.0331, 0.0227, 0.0034, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 5e-04, 0, 0.0028, 0.0047, 5e-04, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 5e-04, 0, 0.0028, 0.0047, 5e-04, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0071, 0, 0, 0, 0, 0.0141, 0, 0.0037, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0475, 0.0786, 0.1765, 0.0906, 0.0083, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0475, 0.0786, 0.1765, 0.0906, 0.0083, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0705, 0.065, 0.0629, 0.0705, 0.1129, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0046, 0.0021, 0.0041, 0, 0, 0, 0, 0.0074, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0046, 0.0021, 0.0041, 0, 0, 0, 0, 0.0074, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0123, 0.0116, 0.004, 0.0083, 0.0015, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0011, 0.0101, 0, 0.0061, 0, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0011, 0.0101, 0, 0.0061, 0, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0.0048, 0.0021, 0, 0, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.262, 0.3094, 0.3366, 0.3853, 0.3204, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.4411, 0.3607, 0.3534, 0.5803, 0.4079, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0197, 0, 0, 0, 0, 0.0786, 0, 0, 0), :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0197, 0, 0, 0, 0, 0.0786, 0, 0, 0), :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0.006, 0, 0, 0, 4e-04, 0.005, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0241, 0.1613, 0.0185, 0, 0.0095, 0, 0.2372, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0241, 0.1613, 0.0185, 0, 0.0095, 0, 0.2372, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0641, 0.0397, 0.0027, 0.088, 0.0037, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.035, 0.0105, 0, 0.0159, 0, 0, 0, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.035, 0.0105, 0, 0.0159, 0, 0, 0, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0177, 0.0041, 0, 0.0032, 0.0035, 0, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0268, 0.0473, 0, 0.0019, 0, 0.1396, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0268, 0.0473, 0, 0.0019, 0, 0.1396, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0.0124, 0.0165, 0, 0, 0.0225, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0553, 0.0671, 0, 0.006, 0, 0, 0.0093, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0553, 0.0671, 0, 0.006, 0, 0, 0.0093, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.0431, 0, 0.0725, 0.0111, 0, 0.0385, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.1455, 0.0523, 0.062, 0.1139, 0.1092, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0098, 0, 0.0715, 0.0305, 0.2699, 0.0825, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.6273, 0.3138, 0.1276, 0.1701, 0.4489, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.2353, 0.1295, 0.2008, 0.0964, 0.5609, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0312, 0.003, 0.0215, 0.2304, 0.0427, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0312, 0.003, 0.0215, 0.2304, 0.0427, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0221, 0.0417, 0.0456, 0, 0.0407, 0.0427, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0494, 0.0187, 0.0183, 0.1651, 0.0516, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0494, 0.0187, 0.0183, 0.1651, 0.0516, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.037, 0.0546, 0.0541, 0, 0.0491, 0.0533, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.0458, 0, 0, 0, 0.0902, 0.0081, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.0458, 0, 0, 0, 0.0902, 0.0081, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.0254, 0, 0.0329, 0, 0, 0, 0.0158, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0353, 0, 0, 0, 0, 0.1113, 0.0158, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0353, 0, 0, 0, 0, 0.1113, 0.0158, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0.0075, 0.0011, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0241, 0.0074, 0, 0, 0, 0.1084, 1e-04, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0241, 0.0074, 0, 0, 0, 0.1084, 1e-04, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 9e-04, 0, 0, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0958, 0.0733, 0.1585, 0.2817, 0.2536, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0958, 0.0733, 0.1585, 0.2817, 0.2536, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0602, 0.0506, 0.136, 0, 0.0453, 0.196, :
## cannot compute exact p-value with ties
CIBERSORT
## Warning in wilcox.test.default(c(0.050715897773675, 0.0589216303571212, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.050715897773675, 0.0589216303571212, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0318966041555209, 0.0508095079022262, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 9e-04, 0, 0, 0, 0, 0, 0),
## c(0.00998927271963148, : cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 9e-04, 0, 0, 0, 0, 0, 0), c(0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
## 0.150595294100848, : cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.00732318173480844, 0.0133312289047236, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.00732318173480844, 0.0133312289047236, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.00822387484636926, 0, 0, 0,
## 0.00137467512825642, : cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.089000329769136, 0.0556561921214293, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.089000329769136, 0.0556561921214293, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0457651525286324, 0.0229009785784177, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), c(0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), c(0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0171137861131678, 0.0174792417076714, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0171137861131678, 0.0174792417076714, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0.00505752713538209, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0720692087262833, 0.0311107582749746, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0602878161955419, 0.0854413624332458, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.00387945492287396, 0.0183321857070058, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.00387945492287396, 0.0183321857070058, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.00812540810014259, 0, 0.00566558068227889, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), c(0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), c(0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0602090338783283, 0.0235375184477379, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0602090338783283, 0.0235375184477379, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0261781922446611, 0.0369721518040315, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0223605215308501, 0.020772858816945, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0223605215308501, 0.020772858816945, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0720073791097346, 0.038569324836885, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0587348946100486, 0.00181518709696392, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0587348946100486, 0.00181518709696392, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0353323257032854, 0.0574202273437429, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0816614219933261, 0.0355161783744101, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0816614219933261, 0.0355161783744101, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0345224773124627, 0.0305392202633606, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0979241038044601, 0.078250151364972, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0979241038044601, 0.078250151364972, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.110750985718031, 0.109212559537125, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.00705661029649803, 0.00650356714702842, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.00705661029649803, 0.00650356714702842, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0.00782109688406625,
## 0.0739573605083729, : cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0535620408002784, 0, 0.0133267664120756, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0535620408002784, 0, 0.0133267664120756, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0582510627882573, 0.031531502461927, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0422742096194234, 0.109637959013854, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.0422742096194234, 0.109637959013854, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0225370927263392, 0.0700382010163719, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0.0393189644862643,
## 0.158491540070273, : cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0.0393189644862643,
## 0.158491540070273, : cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0131375727202622, 0, 0, 0.0488424637294577, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0131375727202622, 0, 0, 0.0488424637294577, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0.001, 0, 0.0229035270696558, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), c(0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), c(0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 8e-04, 0.0270383100740529, 0, : cannot
## compute exact p-value with ties
quanTIseq
## Warning in wilcox.test.default(c(0.00399975735091767, 0.0202122943787033, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.00399975735091767, 0.0202122943787033, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0106234230323736, 0.0120660484795853, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0165097760250007, 0.0279658857720924, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0165097760250007, 0.0279658857720924, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0331792192078885, 0.0721540962543036, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), c(0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0), c(0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, : cannot
## compute exact p-value with ties## Warning in wilcox.test.default(c(0.0299625120235453, 0.0251496407576396, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0299625120235453, 0.0251496407576396, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.0232240531090068, 0.0377878981728211, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0.0884899506757721,
## 7.21432290820029e-05, : cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0, 0.0884899506757721,
## 7.21432290820029e-05, : cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.00904689655345614, 0, 0.0479150231008549, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.00435471117444115, 0.0366003452803578, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0.00985972201941608, 0.00143522968424654, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0.0228099673146307, 0, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0.0228099673146307, 0, 0, :
## cannot compute exact p-value with ties## Warning in wilcox.test.default(c(0, 0, 0, 0, 0, 0.0178381323159788,
## 0.0304709115102939, : cannot compute exact p-value with ties
MCP counter
## Warning in wilcox.test.default(c(0.352, 0.20425, 0.3145, 0.039375, 0.356125, :
## cannot compute exact p-value with ties
Differential gene expression analysis
## Unlist done## Labeling done## Filtering done## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors## Design done## Warning in DESeqDataSet(se, design = design, ignoreRank): some variables in
## design formula are characters, converting to factors## Warning: Setting row names on a tibble is deprecated.## vsd symbols done## using pre-existing size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 2240 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing## DESeq done## using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014).
##
## Note that type='apeglm' and type='ashr' have shown to have less bias than type='normal'.
## See ?lfcShrink for more details on shrinkage type, and the DESeq2 vignette.
## Reference: https://doi.org/10.1093/bioinformatics/bty895## res symbols done## list doneDE results
## Pathway enrichment analysis fGSEA CANARY Good prognosis (G) is the reference. When sample is P, pathways shown below are up- or down- regulated
## `summarise()` ungrouping output (override with `.groups` argument)## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm
## = 1000): You are trying to run fgseaSimple. It is recommended to use
## fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument
## in the fgsea function call.## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm
## = 1000): You are trying to run fgseaSimple. It is recommended to use
## fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument
## in the fgsea function call.## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm
## = 1000): You are trying to run fgseaSimple. It is recommended to use
## fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument
## in the fgsea function call.## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm
## = 1000): You are trying to run fgseaSimple. It is recommended to use
## fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument
## in the fgsea function call.## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm
## = 1000): You are trying to run fgseaSimple. It is recommended to use
## fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument
## in the fgsea function call.## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm
## = 1000): You are trying to run fgseaSimple. It is recommended to use
## fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument
## in the fgsea function call.## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm
## = 1000): You are trying to run fgseaSimple. It is recommended to use
## fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument
## in the fgsea function call.## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm
## = 1000): You are trying to run fgseaSimple. It is recommended to use
## fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument
## in the fgsea function call.## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm
## = 1000): You are trying to run fgseaSimple. It is recommended to use
## fgseaMultilevel. To run fgseaMultilevel, you need to remove the nperm argument
## in the fgsea function call.## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize, gseaParam, : There are ties in the preranked stats (0.04% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## # A tibble: 13 x 8
## pathway pval padj ES NES nMoreExtreme size state
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <chr>
## 1 HALLMARK_E2F_TARGETS 0.00154 0.0159 0.539 2.50 0 191 up
## 2 HALLMARK_G2M_CHECKPOINT 0.00156 0.0159 0.523 2.42 0 187 up
## 3 HALLMARK_TGF_BETA_SIGNA… 0.00230 0.0159 -0.512 -2.06 0 54 down
## 4 HALLMARK_MYC_TARGETS_V1 0.00155 0.0159 0.437 2.03 0 189 up
## 5 HALLMARK_GLYCOLYSIS 0.00156 0.0159 0.435 2.01 0 188 up
## 6 HALLMARK_MYC_TARGETS_V2 0.00176 0.0159 0.496 1.91 0 57 up
## 7 HALLMARK_MYOGENESIS 0.00287 0.0159 -0.367 -1.80 0 190 down
## 8 HALLMARK_ADIPOGENESIS 0.00281 0.0159 -0.330 -1.61 0 183 down
## 9 HALLMARK_HEME_METABOLISM 0.00278 0.0159 -0.322 -1.57 0 179 down
## 10 HALLMARK_FATTY_ACID_MET… 0.00545 0.0252 -0.336 -1.60 1 147 down
## 11 HALLMARK_XENOBIOTIC_MET… 0.00554 0.0252 -0.296 -1.45 1 188 down
## 12 HALLMARK_MTORC1_SIGNALI… 0.00613 0.0255 0.314 1.46 3 190 up
## 13 HALLMARK_CHOLESTEROL_HO… 0.00962 0.0370 -0.363 -1.53 3 69 down
## # A tibble: 30 x 8
## pathway pval padj ES NES nMoreExtreme size state
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <chr>
## 1 chr7p22 0.00157 0.0256 0.645 2.67 0 85 up
## 2 chr12q15 0.00172 0.0256 0.703 2.36 0 34 up
## 3 MT 0.00170 0.0256 0.709 2.34 0 31 up
## 4 chr12q14 0.00166 0.0256 0.617 2.34 0 56 up
## 5 chr8p22 0.00228 0.0256 -0.647 -2.18 0 25 down
## 6 chr7p15 0.00163 0.0256 0.562 2.18 0 61 up
## 7 chr13q34 0.00255 0.0256 -0.536 -2.14 0 54 down
## 8 chr8p21 0.00272 0.0256 -0.465 -2.10 0 88 down
## 9 chr17q23 0.00264 0.0256 -0.498 -2.08 0 64 down
## 10 chr9q33 0.00281 0.0256 -0.453 -2.08 0 104 down
## # … with 20 more rows
## # A tibble: 30 x 8
## pathway pval padj ES NES nMoreExtreme size state
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <chr>
## 1 SOTIRIOU_BREAST_CANCER_G… 0.00157 0.0383 0.664 2.99 0 138 up
## 2 ROSTY_CERVICAL_CANCER_PR… 0.00161 0.0383 0.676 2.98 0 130 up
## 3 KOBAYASHI_EGFR_SIGNALING… 0.00150 0.0383 0.594 2.85 0 239 up
## 4 LEE_EARLY_T_LYMPHOCYTE_UP 0.00161 0.0383 0.664 2.80 0 95 up
## 5 WHITEFORD_PEDIATRIC_CANC… 0.00161 0.0383 0.650 2.79 0 108 up
## 6 KONG_E2F3_TARGETS 0.00169 0.0383 0.656 2.72 0 88 up
## 7 DUTERTRE_ESTRADIOL_RESPO… 0.00146 0.0383 0.543 2.68 0 305 up
## 8 CROONQUIST_IL6_DEPRIVATI… 0.00167 0.0383 0.642 2.67 0 91 up
## 9 FLORIO_NEOCORTEX_BASAL_R… 0.00157 0.0383 0.579 2.66 0 171 up
## 10 SHEDDEN_LUNG_CANCER_POOR… 0.00145 0.0383 0.523 2.65 0 426 up
## # … with 20 more rows
## # A tibble: 0 x 8
## # … with 8 variables: pathway <chr>, pval <dbl>, padj <dbl>, ES <dbl>,
## # NES <dbl>, nMoreExtreme <dbl>, size <int>, state <chr>
## # A tibble: 30 x 8
## pathway pval padj ES NES nMoreExtreme size state
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <chr>
## 1 MODULE_54 0.00151 0.0135 0.599 2.89 0 241 up
## 2 GNF2_CCNA2 0.00170 0.0135 0.704 2.79 0 65 up
## 3 GNF2_MCM4 0.00172 0.0135 0.738 2.78 0 52 up
## 4 GNF2_BUB1B 0.00177 0.0135 0.747 2.77 0 49 up
## 5 GNF2_SMC4L1 0.00169 0.0135 0.675 2.77 0 80 up
## 6 GNF2_RRM1 0.00172 0.0135 0.667 2.76 0 86 up
## 7 GNF2_CDC20 0.00174 0.0135 0.730 2.75 0 53 up
## 8 GNF2_PCNA 0.00170 0.0135 0.693 2.74 0 65 up
## 9 GNF2_RRM2 0.00174 0.0135 0.771 2.74 0 39 up
## 10 GNF2_CCNB2 0.00175 0.0135 0.713 2.69 0 54 up
## # … with 20 more rows
## # A tibble: 0 x 8
## # … with 8 variables: pathway <chr>, pval <dbl>, padj <dbl>, ES <dbl>,
## # NES <dbl>, nMoreExtreme <dbl>, size <int>, state <chr>
## # A tibble: 0 x 8
## # … with 8 variables: pathway <chr>, pval <dbl>, padj <dbl>, ES <dbl>,
## # NES <dbl>, nMoreExtreme <dbl>, size <int>, state <chr>
## # A tibble: 30 x 8
## pathway pval padj ES NES nMoreExtreme size state
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <int> <chr>
## 1 GSE15750_DAY6_VS_DAY10_… 0.00153 0.0484 0.570 2.64 0 188 up
## 2 GSE15750_DAY6_VS_DAY10_… 0.00154 0.0484 0.572 2.63 0 181 up
## 3 GSE21063_WT_VS_NFATC1_K… 0.00155 0.0484 0.565 2.60 0 178 up
## 4 GSE24634_TREG_VS_TCONV_… 0.00153 0.0484 0.535 2.47 0 183 up
## 5 GSE22886_NAIVE_TCELL_VS… 0.00292 0.0484 -0.496 -2.40 0 191 down
## 6 GSE30962_PRIMARY_VS_SEC… 0.00153 0.0484 0.514 2.37 0 184 up
## 7 GSE27241_WT_VS_RORGT_KO… 0.00156 0.0484 0.534 2.37 0 142 up
## 8 GSE13547_CTRL_VS_ANTI_I… 0.00152 0.0484 0.513 2.36 0 174 up
## 9 GSE11057_CD4_CENT_MEM_V… 0.00292 0.0484 -0.496 -2.36 0 180 down
## 10 GSE24634_TEFF_VS_TCONV_… 0.00152 0.0484 0.510 2.36 0 192 up
## # … with 20 more rows
## # A tibble: 0 x 8
## # … with 8 variables: pathway <chr>, pval <dbl>, padj <dbl>, ES <dbl>,
## # NES <dbl>, nMoreExtreme <dbl>, size <int>, state <chr>